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Coexpression cluster:C378: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.765264,0.0178292,0.0508589,0.115973,0.339547,0.115097,0.158494,0.143186,0.0102233,0.279671,1.11439,0.185675,0.347228,0.15157,0.954725,0.168654,0.312612,0.0224301,0.00655392,0.190158,0.0508801,0.24114,0.357972,0.59814,0.0686902,0.200538,0.0217339,1.1843,0.0379339,0.126986,0.62111,0.341173,0.368873,0.19749,0.114422,0.148273,0.503302,0.115713,0.438438,0.00794539,1.60557,0.0813515,0.000190001,0.948411,3.19491e-06,0.0625393,0.933594,0.0941929,0.00125066,0.0379734,0.210045,0.16639,0.00110498,0.402924,0.532737,0.153325,0.0392903,0.417969,0.00269451,0.133632,0.373766,0.484178,0.0102922,0.291591,0.171703,0.266103,0.611096,0.954146,2.41271,0.800453,1.40858,0.787511,0.252061,0.530988,0.778739,0.0715484,0.0186098,0.278987,0.330507,0.0661366,0.628781,2.20351,3.77958,0.0541031,0.486416,0.00230791,0.0171531,0.576491,0.227861,1.04966,0.695939,0.463366,0.933511,0.0778659,0.0372148,0.689984,0.382031,0.388689,0.231068,0.0955711,0.232609,0.349965,0.384158,0.846519,4.66982,0.0972887,0.303327,2.06286,1.33704,0.131219,0.202118,0.381914,0.0488919,0.104282,0.652077,0.498844,0.851347,0.297213,0.264397,0.650475,1.30006,0.226179,0.113636,0.178598,0.753832,0.27955,0.914845,0.942299,0.561176,0.222109,0.463953,4.98075,3.52057,3.83496,1.68616,0.00211008,0.291054,0.11017,2.70889,1.49486,1.10037,0.634967,0.155698,1.00264,0.259011,0.129436,0.690601,1.33792,0.0798475,0.0164579,0.00572822,0.00134497,0.464277,0.129488,0.160304,0.829202,0.216727,0.133083,0.0687147,0.0571684,0.633868,2.95819,0.329893,0.0584032,2.92733,0.50974,0.014267,0.157687,0.00392029
|tfbs_overrepresentation_for_novel_motifs=0.765264,0.0178292,0.0508589,0.115973,0.339547,0.115097,0.158494,0.143186,0.0102233,0.279671,1.11439,0.185675,0.347228,0.15157,0.954725,0.168654,0.312612,0.0224301,0.00655392,0.190158,0.0508801,0.24114,0.357972,0.59814,0.0686902,0.200538,0.0217339,1.1843,0.0379339,0.126986,0.62111,0.341173,0.368873,0.19749,0.114422,0.148273,0.503302,0.115713,0.438438,0.00794539,1.60557,0.0813515,0.000190001,0.948411,3.19491e-06,0.0625393,0.933594,0.0941929,0.00125066,0.0379734,0.210045,0.16639,0.00110498,0.402924,0.532737,0.153325,0.0392903,0.417969,0.00269451,0.133632,0.373766,0.484178,0.0102922,0.291591,0.171703,0.266103,0.611096,0.954146,2.41271,0.800453,1.40858,0.787511,0.252061,0.530988,0.778739,0.0715484,0.0186098,0.278987,0.330507,0.0661366,0.628781,2.20351,3.77958,0.0541031,0.486416,0.00230791,0.0171531,0.576491,0.227861,1.04966,0.695939,0.463366,0.933511,0.0778659,0.0372148,0.689984,0.382031,0.388689,0.231068,0.0955711,0.232609,0.349965,0.384158,0.846519,4.66982,0.0972887,0.303327,2.06286,1.33704,0.131219,0.202118,0.381914,0.0488919,0.104282,0.652077,0.498844,0.851347,0.297213,0.264397,0.650475,1.30006,0.226179,0.113636,0.178598,0.753832,0.27955,0.914845,0.942299,0.561176,0.222109,0.463953,4.98075,3.52057,3.83496,1.68616,0.00211008,0.291054,0.11017,2.70889,1.49486,1.10037,0.634967,0.155698,1.00264,0.259011,0.129436,0.690601,1.33792,0.0798475,0.0164579,0.00572822,0.00134497,0.464277,0.129488,0.160304,0.829202,0.216727,0.133083,0.0687147,0.0571684,0.633868,2.95819,0.329893,0.0584032,2.92733,0.50974,0.014267,0.157687,0.00392029
|tfbs_overrepresentation_jaspar=MA0003.1;0.000253048,MA0004.1;0.102156,MA0006.1;0.336062,MA0007.1;0.0928194,MA0009.1;0.429031,MA0014.1;4.19875e-07,MA0017.1;0.0494581,MA0019.1;0.553399,MA0024.1;0.343215,MA0025.1;0.544326,MA0027.1;1.97447,MA0028.1;1.02106,MA0029.1;1.68166,MA0030.1;0.349473,MA0031.1;0.299024,MA0038.1;0.160193,MA0040.1;0.363365,MA0041.1;1.75008,MA0042.1;0.0954223,MA0043.1;0.429296,MA0046.1;0.419892,MA0048.1;0.0304052,MA0050.1;1.08896,MA0051.1;0.157595,MA0052.1;0.366488,MA0055.1;0.000216937,MA0056.1;0,MA0057.1;0.00104659,MA0058.1;0.0589349,MA0059.1;0.0584293,MA0060.1;0.0102756,MA0061.1;0.0365548,MA0063.1;0,MA0066.1;0.160456,MA0067.1;0.711124,MA0068.1;0.0207462,MA0069.1;0.416668,MA0070.1;0.407339,MA0071.1;0.137013,MA0072.1;0.403605,MA0073.1;2.08777e-14,MA0074.1;0.925184,MA0076.1;0.86263,MA0077.1;0.397221,MA0078.1;1.18649,MA0081.1;0.0584929,MA0083.1;0.435361,MA0084.1;0.887042,MA0087.1;0.401577,MA0088.1;0.000184094,MA0089.1;0,MA0090.1;0.0714597,MA0091.1;0.103495,MA0092.1;0.287838,MA0093.1;0.037369,MA0095.1;0,MA0098.1;0,MA0100.1;0.168841,MA0101.1;0.0383945,MA0103.1;0.135646,MA0105.1;0.0554264,MA0106.1;0.18641,MA0107.1;0.0191145,MA0108.2;0.296685,MA0109.1;0,MA0111.1;0.0774258,MA0113.1;0.197248,MA0114.1;0.0180618,MA0115.1;0.640975,MA0116.1;0.0198524,MA0117.1;0.460927,MA0119.1;0.0523174,MA0122.1;0.483183,MA0124.1;2.4987,MA0125.1;0.528543,MA0130.1;0,MA0131.1;0.23543,MA0132.1;0,MA0133.1;0,MA0135.1;0.454747,MA0136.1;0.955971,MA0139.1;0.00558827,MA0140.1;0.135474,MA0141.1;0.0577507,MA0142.1;0.275028,MA0143.1;0.197366,MA0144.1;0.184993,MA0145.1;0.0672961,MA0146.1;2.84534e-06,MA0147.1;0.0206136,MA0148.1;1.21956,MA0149.1;0.129939,MA0062.2;0.378334,MA0035.2;0.420168,MA0039.2;7.46366e-09,MA0138.2;0.223528,MA0002.2;0.00869004,MA0137.2;0.677111,MA0104.2;0.0507482,MA0047.2;1.60511,MA0112.2;0.00190071,MA0065.2;0.00254951,MA0150.1;0.52088,MA0151.1;0,MA0152.1;0.139287,MA0153.1;0.513757,MA0154.1;0.0528121,MA0155.1;0.283654,MA0156.1;1.99958,MA0157.1;0.254856,MA0158.1;0,MA0159.1;0.0207537,MA0160.1;0.123537,MA0161.1;0,MA0162.1;3.64416e-05,MA0163.1;0.00107556,MA0164.1;1.12038,MA0080.2;0.0373957,MA0018.2;0.187315,MA0099.2;0.850633,MA0079.2;9.57336e-12,MA0102.2;0.922526,MA0258.1;0.170584,MA0259.1;0.0225104,MA0442.1;0
}}
}}

Revision as of 19:07, 22 January 2013


Full id: C378_Smooth_mesenchymal_placenta_clear_leiomyoma_renal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr3:119012895..119012908,+p6@ARHGAP31
Hg19::chr7:93515840..93515856,-p@chr7:93515840..93515856
-
Hg19::chr7:93515914..93515935,-p@chr7:93515914..93515935
-
Hg19::chr7:93515962..93515978,-p@chr7:93515962..93515978
-
Hg19::chr7:93516018..93516037,-p@chr7:93516018..93516037
-
Hg19::chr7:93516035..93516056,+p1@CU675118
Hg19::chr7:93516064..93516108,-p@chr7:93516064..93516108
-
Hg19::chr7:93516178..93516195,-p@chr7:93516178..93516195
-
Hg19::chr7:93516564..93516575,+p@chr7:93516564..93516575
+
Hg19::chr7:93516582..93516600,+p@chr7:93516582..93516600
+
Hg19::chr7:93516601..93516634,+p@chr7:93516601..93516634
+
Hg19::chr7:93516618..93516631,-p@chr7:93516618..93516631
-
Hg19::chr7:93516635..93516656,-p@chr7:93516635..93516656
-
Hg19::chr7:93516672..93516693,+p@chr7:93516672..93516693
+
Hg19::chr7:93516698..93516745,-p@chr7:93516698..93516745
-
Hg19::chr7:93518340..93518370,+p@chr7:93518340..93518370
+
Hg19::chr7:93518374..93518429,-p@chr7:93518374..93518429
-
Hg19::chr7:93518433..93518444,-p@chr7:93518433..93518444
-
Hg19::chr7:93518473..93518503,+p@chr7:93518473..93518503
+
Hg19::chr7:93518492..93518540,-p@chr7:93518492..93518540
-
Hg19::chr7:93519471..93519485,-p5@TFPI2
Hg19::chr7:93519497..93519525,-p2@TFPI2
Hg19::chr7:93519528..93519538,-p7@TFPI2
Hg19::chr7:93519532..93519563,+p@chr7:93519532..93519563
+
Hg19::chr7:93519562..93519586,-p4@TFPI2
Hg19::chr7:93519576..93519598,+p@chr7:93519576..93519598
+
Hg19::chr7:93519591..93519595,-p9@TFPI2
Hg19::chr7:93519597..93519625,-p3@TFPI2
Hg19::chr7:93520056..93520072,-p1@TFPI2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0007596blood coagulation0.0115683504062169
GO:0050817coagulation0.0115683504062169
GO:0007599hemostasis0.0115683504062169
GO:0005201extracellular matrix structural constituent0.0115683504062169
GO:0050878regulation of body fluid levels0.0115683504062169
GO:0042060wound healing0.0115683504062169
GO:0004867serine-type endopeptidase inhibitor activity0.0127163546450018
GO:0004866endopeptidase inhibitor activity0.0156599552572707
GO:0030414protease inhibitor activity0.0156599552572707
GO:0004857enzyme inhibitor activity0.0186771458848463
GO:0005578proteinaceous extracellular matrix0.0186771458848463
GO:0009611response to wounding0.0186771458848463
GO:0009605response to external stimulus0.0257995272124555
GO:0044421extracellular region part0.0336630166019074
GO:0065008regulation of biological quality0.0336630166019074
GO:0006950response to stress0.0404671494171671



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue5.58e-3162
striated muscle tissue5.58e-3162
myotome5.58e-3162
artery3.35e-3042
arterial blood vessel3.35e-3042
arterial system3.35e-3042
somite6.36e-3071
presomitic mesoderm6.36e-3071
presumptive segmental plate6.36e-3071
dermomyotome6.36e-3071
trunk paraxial mesoderm6.36e-3071
muscle tissue1.50e-2964
musculature1.50e-2964
musculature of body1.50e-2964
paraxial mesoderm2.73e-2972
presumptive paraxial mesoderm2.73e-2972
dense mesenchyme tissue1.13e-2873
splanchnic layer of lateral plate mesoderm3.14e-2883
epithelial vesicle3.96e-2778
multilaminar epithelium4.04e-2783
epithelial tube open at both ends2.10e-2659
blood vessel2.10e-2659
blood vasculature2.10e-2659
vascular cord2.10e-2659
systemic artery6.69e-2633
systemic arterial system6.69e-2633
vessel2.18e-2268
unilaminar epithelium3.91e-22148
vasculature1.84e-2178
vascular system1.84e-2178
trunk mesenchyme5.99e-21122
epithelial tube1.35e-20117
cardiovascular system2.45e-19109
circulatory system2.14e-18112
mesenchyme2.56e-17160
entire embryonic mesenchyme2.56e-17160
mesoderm3.97e-15315
mesoderm-derived structure3.97e-15315
presumptive mesoderm3.97e-15315
trunk3.78e-12199
smooth muscle tissue1.34e-1115
epithelium2.24e-11306
aorta3.20e-1121
aortic system3.20e-1121
cell layer4.74e-11309
blood vessel smooth muscle8.05e-1110
arterial system smooth muscle8.05e-1110
artery smooth muscle tissue8.05e-1110
aorta smooth muscle tissue8.05e-1110
female gonad1.29e-1013
organism subdivision2.58e-09264
thoracic segment blood vessel7.11e-095
subclavian artery7.11e-095
female organism2.47e-0841
trunk blood vessel2.49e-087
heart blood vessel2.78e-085
coronary vessel2.78e-085
right ovary5.84e-085
female reproductive organ9.24e-0837
female reproductive system9.24e-0837
heart9.34e-0824
primitive heart tube9.34e-0824
primary heart field9.34e-0824
anterior lateral plate mesoderm9.34e-0824
heart tube9.34e-0824
heart primordium9.34e-0824
cardiac mesoderm9.34e-0824
cardiogenic plate9.34e-0824
heart rudiment9.34e-0824
anatomical conduit1.32e-07240
tube1.39e-07192
left ovary2.77e-074
reproductive structure5.54e-0759
reproductive system5.54e-0759
multi-tissue structure6.50e-07342
gonad7.61e-0721
indifferent external genitalia7.61e-0721

Disease
Ontology termp-valuen


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.000253048
MA0004.10.102156
MA0006.10.336062
MA0007.10.0928194
MA0009.10.429031
MA0014.14.19875e-07
MA0017.10.0494581
MA0019.10.553399
MA0024.10.343215
MA0025.10.544326
MA0027.11.97447
MA0028.11.02106
MA0029.11.68166
MA0030.10.349473
MA0031.10.299024
MA0038.10.160193
MA0040.10.363365
MA0041.11.75008
MA0042.10.0954223
MA0043.10.429296
MA0046.10.419892
MA0048.10.0304052
MA0050.11.08896
MA0051.10.157595
MA0052.10.366488
MA0055.10.000216937
MA0056.10
MA0057.10.00104659
MA0058.10.0589349
MA0059.10.0584293
MA0060.10.0102756
MA0061.10.0365548
MA0063.10
MA0066.10.160456
MA0067.10.711124
MA0068.10.0207462
MA0069.10.416668
MA0070.10.407339
MA0071.10.137013
MA0072.10.403605
MA0073.12.08777e-14
MA0074.10.925184
MA0076.10.86263
MA0077.10.397221
MA0078.11.18649
MA0081.10.0584929
MA0083.10.435361
MA0084.10.887042
MA0087.10.401577
MA0088.10.000184094
MA0089.10
MA0090.10.0714597
MA0091.10.103495
MA0092.10.287838
MA0093.10.037369
MA0095.10
MA0098.10
MA0100.10.168841
MA0101.10.0383945
MA0103.10.135646
MA0105.10.0554264
MA0106.10.18641
MA0107.10.0191145
MA0108.20.296685
MA0109.10
MA0111.10.0774258
MA0113.10.197248
MA0114.10.0180618
MA0115.10.640975
MA0116.10.0198524
MA0117.10.460927
MA0119.10.0523174
MA0122.10.483183
MA0124.12.4987
MA0125.10.528543
MA0130.10
MA0131.10.23543
MA0132.10
MA0133.10
MA0135.10.454747
MA0136.10.955971
MA0139.10.00558827
MA0140.10.135474
MA0141.10.0577507
MA0142.10.275028
MA0143.10.197366
MA0144.10.184993
MA0145.10.0672961
MA0146.12.84534e-06
MA0147.10.0206136
MA0148.11.21956
MA0149.10.129939
MA0062.20.378334
MA0035.20.420168
MA0039.27.46366e-09
MA0138.20.223528
MA0002.20.00869004
MA0137.20.677111
MA0104.20.0507482
MA0047.21.60511
MA0112.20.00190071
MA0065.20.00254951
MA0150.10.52088
MA0151.10
MA0152.10.139287
MA0153.10.513757
MA0154.10.0528121
MA0155.10.283654
MA0156.11.99958
MA0157.10.254856
MA0158.10
MA0159.10.0207537
MA0160.10.123537
MA0161.10
MA0162.13.64416e-05
MA0163.10.00107556
MA0164.11.12038
MA0080.20.0373957
MA0018.20.187315
MA0099.20.850633
MA0079.29.57336e-12
MA0102.20.922526
MA0258.10.170584
MA0259.10.0225104
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
RAD21#588593.213631208934720.001208593323296330.00819106282230664



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C378&oldid=2568889"